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- W3043149968 abstract "Abstract Motivation Graph representations of genomes are capable of expressing more genetic variation and can therefore better represent a population than standard linear genomes. However, due to the greater complexity of genome graphs relative to linear genomes, some functions that are trivial on linear genomes become much more difficult in genome graphs. Calculating distance is one such function that is simple in a linear genome but complicated in a graph context. In read mapping algorithms such distance calculations are fundamental to determining if seed alignments could belong to the same mapping. Results We have developed an algorithm for quickly calculating the minimum distance between positions on a sequence graph using a minimum distance index. We have also developed an algorithm that uses the distance index to cluster seeds on a graph. We demonstrate that our implementations of these algorithms are efficient and practical to use for a new generation of mapping algorithms based upon genome graphs. Availability and implementation Our algorithms have been implemented as part of the vg toolkit and are available at https://github.com/vgteam/vg." @default.
- W3043149968 created "2020-07-23" @default.
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- W3043149968 date "2020-07-01" @default.
- W3043149968 modified "2023-10-17" @default.
- W3043149968 title "Distance indexing and seed clustering in sequence graphs" @default.
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- W3043149968 doi "https://doi.org/10.1093/bioinformatics/btaa446" @default.
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